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Mesquite installation for UNIX/LINUX

Requirements: JRE or JDK 1.8 (java.com/download). (It is best to get the Sun-Oracle Java VM; Mesquite does not run on some third-party virtual machines.)  At the moment, Mesquite does not run on Linux with Oracle Java version 11 and above. This is due to a bug in Oracle Java that causes Mesquite to crash during startup with a StackOverflowError. The only workaround we know is to use Java version 8 (i.e. 1.8) which is available from java.com. You may need to make adjustments so that your system knows to use Java 8 (e.g., see instructions here http://www.ormbunkar.se/aliview/#java8install).
Instructions:
  1. If you have an older version of Mesquite, you may want to delete it (by deleting Mesquite_Folder), so as to avoid getting confused as to what version of Mesquite is starting up. First, however, you may want to take from Mesquite_Folder/mesquite any third party packages (e.g., PDAP, TreeSetViz) before deleting the directory.
  2. Download the latest version of Mesquite from the Mesquite Github repository. For Linux, use the file ending in .tgz.
  3. Extract all of the files from the tgz. You will see a Mesquite_Folder. Place this Mesquite_Folder where you want on your hard drive, though if it is in a folder that requires a password for you to modify, you may have problems updating in the future. The contents of Mesquite_Folder should be approximately as follows:


To start Mesquite, execute the mesquite.sh script from the command line:
./mesquite.sh
This should automatically identify your java installation. If you have trouble, you may need to set your JAVA_HOME environment variable. In the uncommon case that you want a java VM to run Mesquite that is different from the VM identified in JAVA_HOME, you may set the MESQUITE_JAVA_HOME environment variable.

Once Mesquite has finished loading, go to the File menu to open a file.

If mesquite.sh fails

In the event that the shell script fails, it may still be posible to run Mesquite manually. You need to ask java to run Mesquite.jar. To start Mesquite you can use jre or java. For instance you could use:
java -cp /home/myuser/Mesquite_Folder -jar Mesquite.jar

This is the minimal way to start Mesquite; a better call would be:

where /home/myuser/Mesquite_Folder could be replaced by whatever is the path to the Mesquite_Folder.

This is the minimal call. A better version would be:

java -Djava.library.path=lib -Djri.ignore.ule="yes" -cp /home/myuser/Mesquite_Folder -jar Mesquite.jar

On some systems the java virtual machine is started by "jre" instead of "java", and thus the command would be:

jre -cp /home/myuser/Mesquite_Folder -jar Mesquite.jar
Depending on your configuration, you may need to give the explicit path to the java virtual machine, as in:
/usr/java/jre1.8.0/bin/java -cp /usr/local/Mesquite_Folder  -jar Mesquite.jar
If you've changed the name of Mesquite_Folder to, for instance, "Mesquite2", you may need to use a command like:
/usr/java/jre1.8.0/bin/java -cp /usr/local/Mesquite2  -jar Mesquite.jar
If you've had to do all this because the shell script isn't working, please let us know what happened, and what you did to make Mesquite work. That way, we can make it easier for the next person.

Window Managers

Mesquite attempts to place windows in particular places on the screen for ease of use, using standard Java calls. Some window managers override this, resulting in haphazard placement of windows. You may need to change your window manager if this sort of thing is happening.

Java Virtual Machines

If your Java is not one made by Oracle or Sun, it may not work well.


If you have multiple JVMs installed, you may need to edit the run_mesquite.sh file to instruct Mesquite where to look for the virtual machine. To do this, open run_mesquite.sh in a text editor and find the line:

java="java"
Replace it (or comment it out, as below, using "#" and append it) with the absolute path to Oracle's JVM (which may be different than the path listed below):
#java="java"
java="PATHTOJAVA/bin/java"
making sure to pay attention to spacing; the script may have problems if there is extra whitespace between "java" & "=". Alternatively, if you don't use the script, but would like to run Mesquite from the Terminal command line, just use the absolute path to the Java VM you prefer when starting Mesquite, as above:
     PATHTOJAVA/bin/java -cp /home/myuser/Mesquite_Folder  -jar Mesquite.jar
More details of issues of using Mesquite under Linux/UNIX are described in the Bugs and Troubleshooting page.

(Please email us at info {at} mesquiteproject.org) with questions or comments about downloading Mesquite).